Is anyone out there writing their own meshes from scratch? I am looking at creating my own mesh in MATLAB and importing it into CFX Pre. I know this was easy and useful in CFX 4.4, but I imagine it will be more complicated in CFX 5.6 because of the unstructured code.

If anyone has any experience with this, do you have any comments on the ease and feasibility?

The trickier bit is creating 2D regions so that you can assign boundary conditions. You have to define faces on your boundaries, what interior elements these faces are attached to, and what element local face number is on the boundary (so that you know which vertices are on the boundary).

I suggest you carefully read through the user defined mesh import documentation. There is an interface for doing this in CFX-5.

I think that maybe Patran neutral format(which is supported by CFX-PRE) can be answer. Instead of defining 2D regions you can simply have 3D regions and group of nodes which treated by CFX-Pre as 2D regions. Patran neutral is text format so you could write your own translator... Interior regions between different domains are created automaticaly.